In the BUILD module molecules can be built from scratch, residues can be changed, chanes prolonged and new residies inserted. An EXIT command word must be applied to return from INTERNAL> to MAIN>.
EXIT START APPEND RESIDUE string(s) INSERT atom-numb RESIDUE string(s) SELE ... END
[ALL]
CHANGE RESIDUE string
FILL
DIHEDRAL
SEGMENT string
SEQUENCE string
CENTER COORDINATES
CALCULATED
ATOM
APPEND nn * (integer string)
APPENDs residues. Residues, when found in the topology library are appended to the end of atom list, however by INSERT they start apearing before the first SELECTED residue. As many as wanted residue names can be given. Each residue name can be preceded by an integer (number of repetitions). Default number of repetitions is 1.
INSERT nn * (integer string)
INSERTs residues. Residues, when found in the topology library are inserted before the first SELECTED residue. The APPEND command adds them to the end of the list. As many as wanted residue names can be specified. Each residue name can be preceded by an integer (number of repetitions). Default number of repetitions is 1.
CHANGE string
CHANGEs the SELECTED residue by converting it into the new specified one. CHANGE acts only on one residue at a time (the first SELECTED residue).
Atoms of the old and new residue are compared by names. The matching atoms in both residues (except hydrogens) keep the old position (COORDINATES), TEMPERATURE factor and crystallographic WEIGHT. The rest of atoms are build from the INTERNAL coordinates data, when they are present in the topology library. Therefore sometimes atoms of the CHANGED residues appear in a weard conformations. To get around this either a RESIDUE should be CHANGED in two steps; in first step into a smaller residue (as ALA) and in second step the newly created residue (ALA) is CHANGED into the desired residue. The other solution is to energetically MINIMIZE such irregular parts.
When a larger range of residues should be changed, then it is recommanded to use combination of RENAME RESIDUE followed by a FILL command in the BUILD module.
FILL
FILLs residues by inserting missing atoms. It acts on the whole SELECTION in contrary to CHANGE. FILL calls CHANGE command within a loop, however it has no parameter (a new RESIDUE NAME). It keeps the current residue names. It can be used for hydrogen atom insertion or when a residue composition of a whole molecule is supposed to be replaced by a new one (in combination with RENAME).
Corrects the bad DIHEDRAL angles resluted from a FILL command by adjusting DIHEDRAL angles of newly defined atoms present in INTERNAL coordinates to the DIHEDRAL angles in the TOPOLOGY library.
SEGMENT string
Sets the name for a newly created SEGMENT. This segment name is used only when a new segment is created that is in combination with START.
SEQUENCE string
Sets a root for SEQUENCE names. Each newly created residue sequence name starts with the root string generating additional characters going from 1 to 9. For example root B generates series B1 ... B9 B10 ... B20 etc.
CENTER COORDINATES 3*real
CALCULATED
ATOM
Sets a CENTER that may be later used when STARTing a new chain.
START
Sets the START flag for the next INSERT or APPEND command. When START flag is set a new RESIDUE chain starts at the specified CENTER. The resulting chain of residues is not connected to already existing atoms.